Characterize AT and GC content throughout genes

[tindinh]

Hi guys,

I am doing a project about finding distribution of AT vs GC throughout genes of human and mouse. The project would like me to answer if there are any common enrichments close to the transcription start site, introns or near 3' end of the gene.

Can you please give me some hints on it? Which data and package can be used? Thank you a lot!

[SylvainL]

Hi,

I see different strategies:
- either you do some window scanning on the whole genome (10 or 20bp, or longer, depends on how precise you want to be) and you report the % for each item..
- either you extract the different region of interest (all the promoters, all in the same orientation and centered to the TSS, same for 3'ends, etc...) and you do an analysis by population...

You can do that in R, using different packages (like ape, or Ringo...)

s.